Script to merge all RS data

This R script is used to merge RS data downloaded the Google Drive folder shared by Bea with the ReSurvey database.

Load libraries

library(tidyverse)
library(here)
library(lubridate)
library(dtplyr)
library(sf)

Read files with RS data from Bea

S2

NDVI, NDMI & other indices

Files downloaded from folder Drive/MOTIVATE-EVEREST/1.VALIDATION/db_Europe/S2/Ene-dic

# Set the folder path
folder_path <- "C:/Data/MOTIVATE/MOTIVATE_RS_data/S2"

# List CSV files
csv_files <- list.files(folder_path, full.names = TRUE, recursive = TRUE)

# Function to extract biogeo and unit from the filename
extract_info <- function(filename) {
  first_word <- strsplit(filename, "_")[[1]][1]
  biogeo <- str_extract(first_word, "^(ALP|ARC|ATL|BOR|CON|MED|PANONIA)")
  unit <- str_remove(first_word, biogeo)
  if (unit == "") unit <- NA_character_
  list(biogeo = biogeo, unit = unit)
}


# Read and process each file
data_list <- lapply(csv_files, function(file) {
  info <- extract_info(basename(file)) # Use only the filename
  
  # Read the file
  df <- read_csv(file) %>%
    # Remove columns that give column type problems when combining data
    select(-starts_with("EUNIS"), -starts_with("ReSurvey")) %>%
    mutate(biogeo = info$biogeo, unit = info$unit)
  
  return(df)
  })

Rows: 1978 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 205 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 41 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 163 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
G2;H2;Avisoh: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)g
Rows: 5074 Columns: 90
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (47): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 922 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (20): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (51): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 95 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 108 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 1417 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 107 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 918 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 125 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
G2;H2;Avisoh: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)g
Rows: 1827 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 130 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 205 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 8 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (10): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, RS_CODE, ReSurvey p,...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (33): EUNISa_2_d, EUNISa_3, EUNISa_3_d, EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 8 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 1188 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (20): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (23): EUNISa_4, EUNISa_4_d, EUNISb_1, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EU...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

# Combine all data
data_RS_S2 <- bind_rows(data_list)

# View the resulting tibble
print(data_RS_S2)

# Counts per biogeo and unit
print(data_RS_S2 %>% count(biogeo, unit), n = 100)

Data cleaning

Keep all indices and metrics in case they are useful.

data_RS_S2 <- data_RS_S2 %>%
  # Keep the columns we need
  select(PlotObserv, biogeo, unit, year, Lat_update, Lon_update,
         starts_with("NDVI"), starts_with("NDMI"), starts_with("NDWI"),
         starts_with("EVI"), starts_with("SAVI")) %>%
  # Rename Lat and Lon, these are only kept in case there is difference with
  # those in the ReSurvey database due to updates based on Ilona's info
  rename(Lat_RS = Lat_update, Lon_RS = Lon_update) %>%
  # Same for year
  rename(year_RS = year) %>%
  # Add column source
  mutate(source = "S2")

Phenology S2

HERE: Do not use so far - wrong!

Landsat

NDVI, NDMI & other indices

# Set the folder path
folder_path <- "C:/Data/MOTIVATE/MOTIVATE_RS_data/Landsat"

# List CSV files
csv_files <- list.files(folder_path, full.names = TRUE, recursive = TRUE)

# Function to extract biogeo and unit from the filename
extract_info <- function(filename) {
  first_word <- strsplit(filename, "_")[[1]][1]
  biogeo <- str_extract(first_word, "^(ALP|ARC|ATL|BOR|CON|MED|PANONIA)")
  unit <- str_remove(first_word, biogeo)
  if (unit == "") unit <- NA_character_
  list(biogeo = biogeo, unit = unit)
}

# Read and process each file
data_list <- lapply(csv_files, function(file) {
  info <- extract_info(basename(file)) # Use only the filename
  
  # Read the file
  df <- read_csv(file) %>%
    # Remove columns that give column type problems when combining data
    select(-starts_with("EUNIS"), -starts_with("ReSurvey")) %>%
    mutate(biogeo = info$biogeo, unit = info$unit)
  
  return(df)
  })

G2;H2;Avisoh: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)g
Rows: 5213 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 423 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 138 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 51 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 117 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 213 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 64 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 92 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
G2;H2;Avisoh: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)g
Rows: 9447 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 6438 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 96 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (24): system:index, EUNISa, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (19): EUNISa_1, EUNISa_4, EUNISa_4_d, EUNISb_1, EUNISb_4, EUNISb_4_d, EUNISc_1, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 99 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 185 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 198 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (20): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (23): EUNISa_4, EUNISa_4_d, EUNISb_1, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EU...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 20 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (12): system:index, EUNISa, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (31): EUNISa_1, EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EU...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2394 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 160 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
G2;H2;Avisoh: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)g
Rows: 2068 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (20): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (23): EUNISa_4, EUNISa_4_d, EUNISb_1, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EU...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
G2;H2;Avisoh: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)g
Rows: 9807 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (26): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (17): EUNISa_4, EUNISa_4_d, EUNISb_1, EUNISb_4, EUNISb_4_d, EUNISc_1, EUNISc_4, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 308 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
G2;H2;Avisoh: One or more parsing issues, call `problems()` on your data frame for details, e.g.:
  dat <- vroom(...)
  problems(dat)g
Rows: 16171 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2239 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (20): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (23): EUNISa_4, EUNISa_4_d, EUNISb_1, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EU...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 82 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (13): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (51): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 10 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 422 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (21): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (22): EUNISa_4, EUNISa_4_d, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EUNISc_1_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 393 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 12 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (10): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, RS_CODE, ReSurvey p,...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (33): EUNISa_2_d, EUNISa_3, EUNISa_3_d, EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 9 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 5 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (14): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 37 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (13): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (51): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (29): EUNISa_4, EUNISa_4_d, EUNISb, EUNISb_1, EUNISb_1_d, EUNISb_2, EUNISb_2_d, ...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Rows: 2042 Columns: 93
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (20): system:index, EUNISa, EUNISa_1, EUNISa_1_d, EUNISa_2, EUNISa_2_d, EUNISa_3...
dbl (50): EVI_max, EVI_mean, EVI_median, EVI_min, EVI_mode, EVI_p10, EVI_p90, EVI_st...
lgl (23): EUNISa_4, EUNISa_4_d, EUNISb_1, EUNISb_4, EUNISb_4_d, EUNISc, EUNISc_1, EU...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

# Combine all data
data_RS_Landsat <- bind_rows(data_list)

# View the resulting tibble
print(data_RS_Landsat)

# Counts per biogeo and unit
print(data_RS_Landsat %>% count(biogeo, unit), n = 100)

Data cleaning

Keep all indices and metrics in case they are useful.

data_RS_Landsat <- data_RS_Landsat %>%
  # Keep the columns we need
  select(PlotObserv, biogeo, unit, year, Lat_update, Lon_update,
         starts_with("NDVI"), starts_with("NDMI"), starts_with("NDWI"),
         starts_with("EVI"), starts_with("SAVI")) %>%
  # Rename Lat and Lon, these are only kept in case there is difference with
  # those in the ReSurvey database due to updates based on Ilona's info
  rename(Lat_RS = Lat_update, Lon_RS = Lon_update) %>%
  # Same for year
  rename(year_RS = year) %>%
  # Add column source
  mutate(source = "Landsat")

TO ADD: Phenology Landsat

Canopy height

data_RS_CH <- read_csv(
  "C:/Data/MOTIVATE/MOTIVATE_RS_data/Canopy_Height_1m/Europe_points_CanopyHeight_1m.csv")

Rows: 425310 Columns: 8
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (2): system:index, .geo
dbl (6): Lat_update, Lon_update, canopy_height, obs_unique, plot_uniqu, year

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

data_RS_CH

Data cleaning CH

data_RS_CH <- data_RS_CH %>%
  # Keep the columns we need
  select(obs_unique, canopy_height)

TBD: Biomass

Read file db_Europa

In this file, there is the correspondence obs_unique - PlotObservationID.

db_Europa <- read_csv(
  here("..", "DB_first_check", "data", "clean","db_Europa_20250107.csv")
  )

Rows: 425310 Columns: 12
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ","
chr (6): Country, RS_CODE, ReSurvey site, ReSurvey plot, Expert System, Location method
dbl (6): PlotObservationID, Lon_updated, Lat_updated, plot_unique_id, year, obs_uniq...

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Sample db_Europa

Read file db_resurv_updated_clean

This is the ReSurvey database after updates (to be continued).

db_resurv <- read_tsv(
  here("..", "DB_first_check","data", "clean","db_resurv_updated_clean.csv"),
  col_types = cols(
    # Dynamically specify EUNIS columns as character
    .default = col_guess(),  # Default guessing for other columns
    EUNISa = col_character(),
    EUNISb = col_character(),
    EUNISc = col_character(),
    EUNISd = col_character(),
    EUNISa_1 = col_character(),
    EUNISa_2 = col_character(),
    EUNISa_3 = col_character(),
    EUNISa_4 = col_character(),
    EUNISb_1 = col_character(),
    EUNISb_2 = col_character(),
    EUNISb_3 = col_character(),
    EUNISb_4 = col_character(),
    EUNISc_1 = col_character(),
    EUNISc_2 = col_character(),
    EUNISc_3 = col_character(),
    EUNISc_4 = col_character(),
    EUNISd_1 = col_character(),
    EUNISd_2 = col_character(),
    EUNISd_3 = col_character(),
    EUNISd_4 = col_character(),
    EUNISa_1_descr = col_character(),
    EUNISb_1_descr = col_character(),
    EUNISc_1_descr = col_character(),
    EUNISd_1_descr = col_character(),
    EUNIS_assignation = col_character(),
    EUNISa_2_descr = col_character(),
    EUNISa_3_descr = col_character(),
    EUNISa_4_descr = col_character(),
    EUNISb_2_descr = col_character(),
    EUNISb_3_descr = col_character(),
    EUNISb_4_descr = col_character(),
    EUNISc_2_descr = col_character(),
    EUNISc_3_descr = col_character(),
    EUNISc_4_descr = col_character(),
    EUNISd_2_descr = col_character(),
    EUNISd_3_descr = col_character(),
    EUNISd_4_descr = col_character()
    )
  )

No parsing issues!

Get sample of ReSurvey database:

db_Europa_sample <- left_join(
  db_resurv %>%
    select(PlotObservationID, RS_CODE, `ReSurvey site`, `ReSurvey plot`,
           Lon_updated,Lat_updated, year,date,
           starts_with("EUNIS"), `Location method`) %>%
    select(-EUNIS_assignation),
  db_Europa %>%
    select(PlotObservationID, Lon_updated, Lat_updated, year, obs_unique_id)
)

Joining with `by = join_by(PlotObservationID, Lon_updated, Lat_updated, year)`

  
print(db_Europa_sample, width = Inf)

Add column PLOT to data to identify unique plots:

db_Europa_sample <- db_Europa_sample %>%
  # Original names give problems, create new vars
  mutate(RS_site = `ReSurvey site`, RS_plot = `ReSurvey plot`) %>%
  # Convert to data.table for faster processing
  lazy_dt() %>%
  # Group by the 3 vars that uniquely identify each plot
  group_by(RS_CODE, RS_site, RS_plot) %>%
  # Create a new variable PLOT for each group
  mutate(PLOT = .GRP) %>%
  # Convert back to tibble
  as_tibble() %>%
  # Remove unneeded vars
  select(-RS_site, -RS_plot)

Keep only habitats F, R, S and Q, and, for each PLOT, keep only the last resurvey:

db_Europa_sample_latest <- db_Europa_sample %>%
  filter(EUNISa_1 %in% c("T", "R", "S", "Q")) %>%
  group_by(PLOT) %>%
  filter(date == max(date)) %>%
  ungroup()

Save as csv for Bea:

write_csv(db_Europa_sample_latest,
          file = "data/clean/db_Europa_sample_latest.csv")

Save as shp to merge with bioregions:

# # Convert to sf object
# db_Europa_sample_latest_sf <- st_as_sf(db_Europa_sample_latest,
#                                        coords = c("Lon_updated", "Lat_updated"), 
#                                        crs = 4326) # WGS84
# st_write(db_Europa_sample_latest_sf,
#          "C:/GIS/MOTIVATE/shapefiles/db_Europa_sample_latest_sf.shp")

Merge RS data and db_Europa_sample_latest

Get only the columns PlotObservationID (original unique identifier) and obs_unique_id (unique identified created by me).

db_Europa_sample_latest <- db_Europa_sample_latest %>%
  select(PlotObservationID, obs_unique_id)

data_RS_S2_ID <- db_Europa_sample_latest %>%
  right_join(data_RS_S2 %>%
               # Rename to be able to join on this column
               rename(PlotObservationID = PlotObserv))

Joining with `by = join_by(PlotObservationID)`

Now we have PlotObservationID in data_RS_S2_ID.

# data_RS_S2_phen_ID <- db_Europa_sample_latest %>%
#   right_join(data_RS_S2_phen %>%
#               # Rename to be able to join on this column
#                rename(PlotObservationID = PlotObserv))

Now we have PlotObservationID in data_RS_S2_phen_ID

data_RS_Landsat_ID <- db_Europa_sample_latest %>%
  right_join(data_RS_Landsat %>%
               # Rename to be able to join on this column
               rename(PlotObservationID = PlotObserv))

Joining with `by = join_by(PlotObservationID)`

Now we have PlotObservationID in data_RS_Landsat_ID.

data_RS_CH_ID <- db_Europa %>%
  select(PlotObservationID, obs_unique_id) %>%
  right_join(data_RS_CH %>%
              # Rename to be able to join on this column
              rename(obs_unique_id = obs_unique))

Joining with `by = join_by(obs_unique_id)`

Now we have PlotObservationID in data_RS_CH_ID.

Merge RS data to the ReSurvey database

For some points, there is data both from S2 and Landsat. In those cases, use the S2 data because it is more precise (10 m vs 30 m).

data_RS_S2_ID <- data_RS_S2_ID %>%
  rename_with(~ paste0(., "_S2"), starts_with("NDVI")) %>%
  rename_with(~ paste0(., "_S2"), starts_with("NDMI")) %>%
  rename_with(~ paste0(., "_S2"), starts_with("NDWI")) %>%
  rename_with(~ paste0(., "_S2"), starts_with("EVI")) %>%
  rename_with(~ paste0(., "_S2"), starts_with("SAVI")) %>%
  select(-source)
data_RS_Landsat_ID <- data_RS_Landsat_ID %>%
  rename_with(~ paste0(., "_Landsat"), starts_with("NDVI")) %>%
  rename_with(~ paste0(., "_Landsat"), starts_with("NDMI")) %>%
  rename_with(~ paste0(., "_Landsat"), starts_with("NDWI")) %>%
  rename_with(~ paste0(., "_Landsat"), starts_with("EVI")) %>%
  rename_with(~ paste0(., "_Landsat"), starts_with("SAVI")) %>%
  select(-source)

Join S2, S2_phen and Landsat data:

data_RS <- data_RS_S2_ID %>% 
  # full_join(data_RS_S2_phen_ID) %>%
  full_join(data_RS_Landsat_ID)

Joining with `by = join_by(PlotObservationID, obs_unique_id, biogeo, unit, year_RS,
Lat_RS, Lon_RS)`

Number of observations with NDVI_max data from both S2 and Landsat:

nrow(data_RS %>% filter(!is.na(NDVI_max_S2) & !is.na(NDVI_max_Landsat)))

[1] 14518

Difference between NDVI_max values from S2 and Landsat:

data_RS %>% filter(!is.na(NDVI_max_S2) & !is.na(NDVI_max_Landsat)) %>%
  mutate(diff_NDVI_max = abs(NDVI_max_S2 - NDVI_max_Landsat)) %>%
  ggplot(aes(x = diff_NDVI_max, fill = paste(biogeo, unit, sep = "-"))) +
  geom_histogram(color = "black") + 
  facet_wrap(~ paste(biogeo, unit, sep = "-")) + theme(legend.position = "none")

data_RS %>% filter(!is.na(NDMI_max_S2) & !is.na(NDMI_max_Landsat)) %>%
  mutate(diff_NDMI_max = abs(NDMI_max_S2 - NDMI_max_Landsat)) %>%
  ggplot(aes(x = diff_NDMI_max, fill = paste(biogeo, unit, sep = "-"))) +
  geom_histogram(color = "black") + 
  facet_wrap(~ paste(biogeo, unit, sep = "-")) + theme(legend.position = "none")

There is a large difference between NDVI values from S2 and Landsat. So far, use the S2 data, but checking with Bea / Jose.

When values are available from both satellites, use S2:

data_RS <- data_RS %>%
  mutate(across(
    matches("^(NDVI|NDMI|NDWI|EVI|SAVI)_(max|mean|median|min|mode|p10|p90|stdDev)_S2$"),
    ~ case_when(
      # If both the current column and the corresponding Landsat column are NA,
      # set to NA_real_
      is.na(.x) & is.na(get(sub("_S2$", "_Landsat", cur_column()))) ~ NA_real_,
      # If the corresponding Landsat column is NA, use the current column's value
      is.na(get(sub("_S2$", "_Landsat", cur_column()))) ~ .x,
      # If the current column is NA, use the corresponding Landsat column's value
      is.na(.x) ~ get(sub("_S2$", "_Landsat", cur_column())),
      # Otherwise, use the current column's value
      TRUE ~ .x
      ), .names = "{col}_combined")) %>%
  rename_with(~ sub("_S2_combined$", "", .), matches("_S2_combined$"))

Get number of points per biogeo and unit:

npoints_bioregion_R <- data_RS %>% count(biogeo, unit) %>%
  mutate(npoints_R = n) %>%
  select(-n)

Read number of points per biogeo and unit from GIS:

npoints_bioregion_GIS <- read_delim(
  "data/clean/Npoints_bioregion.csv", delim = ";"
  ) %>%
  select (BIOGEO, UNIT, Join_Count) %>%
  mutate(biogeo = BIOGEO, unit = str_remove(UNIT, BIOGEO),
         npoints_GIS = Join_Count) %>%
  mutate(biogeo = ifelse(biogeo == "PAN", "PANONIA", biogeo)) %>%
  mutate(unit = ifelse(biogeo == "PANONIA", NA, unit)) %>%
  select(- BIOGEO, - UNIT, -Join_Count)

Rows: 42 Columns: 54
── Column specification ────────────────────────────────────────────────────────────────
Delimiter: ";"
chr (44): name, BIOGEO, UNIT, RS_CODE, RSrvyst, RSrvypl, date, EUNISa, EUNISb, EUNIS...
dbl  (5): OID_, Join_Count, TARGET_FID, code, PLOT
num  (5): AREA, PltObID, year, Shape_Length, Shape_Area

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Merge both and see differences in n points:

npoints_bioregion_merged <- full_join(npoints_bioregion_R,
                                      npoints_bioregion_GIS)

Joining with `by = join_by(biogeo, unit)`

Nice table to email to Bea:

kable(print(npoints_bioregion_merged %>% arrange(biogeo, unit), n = 100))

biogeo	unit	npoints_R	npoints_GIS
ALP	ALPS	5214	5360
ALP	ATRA	423	423
ALP	BALKAN	138	138
ALP	DINARIC	NA	0
ALP	ENNINE	51	54
ALP	NORDIC	117	117
ALP	PYR	213	213
ALP	ROMANIAN	64	64
ANA	TURKEY	NA	0
ARC	ICELAND	NA	0
ARC	NORWAY	92	106
ATL	BENELUX	9447	9530
ATL	BRITAIN	6438	6761
ATL	FRANCE	96	97
ATL	IBERIA	99	99
ATL	IRELAND	NA	0
ATL	NORDIC	NA	0
BLS	BLACKSEA	NA	0
BOR	BALTIC	185	185
BOR	FINLAND	198	240
BOR	NORDIC	20	20
CON	AUSTRIA	2394	2439
CON	BALKAN	160	160
CON	FRANCE	2068	2091
CON	GERMANY	9807	9924
CON	ITALICA	308	312
CON	NORDIC	16171	16172
CON	POLAND	2239	2241
CON	ROMANIA	82	82
MAC	ARONESIA	NA	0
MED	BALEAR	NA	0
MED	BALKAN	NA	0
MED	FRANCE	NA	0
MED	GREECE	10	10
MED	IBERIA	422	422
MED	ITALICA	393	395
MED	PORT	12	12
MED	SICILIA	9	9
MED	TIRRENO	5	5
MED	TURKEY	37	37
PANONIA	NA	2042	2046
STE	PPIC	NA	0

db_resurv_RS <- db_resurv %>%
  left_join(data_RS %>% select(-obs_unique_id)) %>%
  left_join(data_RS_CH_ID %>% select(-obs_unique_id)) %>%
  mutate(S2_data = !is.na(NDVI_max_S2) & !is.na(NDMI_max_S2), 
         Landsat_data = !is.na(NDVI_max_Landsat) & !is.na(NDMI_max_Landsat),
         S2_or_Landsat_data = !is.na(NDVI_max) & !is.na(NDMI_max), 
         # S2_phen_data = !is.na(SOS_DOY),
         CH_data = !is.na(canopy_height)) %>%
  # So far, remove cols for _S2 and _Landsat
  select(-matches("_(S2|Landsat)$"))

Joining with `by = join_by(PlotObservationID)`
Joining with `by = join_by(PlotObservationID)`

db_resurv_RS %>% count(S2_data)

db_resurv_RS %>% count(Landsat_data)

db_resurv_RS %>% count(S2_or_Landsat_data)

db_resurv_RS %>% count(CH_data)

# db_resurv_RS %>% count(S2_phen_data)

Save to clean data

Save clean file for analyses (to be updated continuously due to updates in ReSurvey database and updates on RS data).

write_tsv(db_resurv_RS,here("data", "clean","db_resurv_RS_20250610.csv"))

Session info

sessionInfo()

R version 4.5.0 (2025-04-11 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default
  LAPACK version 3.12.1

locale:
[1] LC_COLLATE=Spanish_Spain.utf8  LC_CTYPE=Spanish_Spain.utf8   
[3] LC_MONETARY=Spanish_Spain.utf8 LC_NUMERIC=C                  
[5] LC_TIME=Spanish_Spain.utf8    

time zone: Europe/Madrid
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] knitr_1.50      sf_1.0-20       dtplyr_1.3.1    here_1.0.1      lubridate_1.9.4
 [6] forcats_1.0.0   stringr_1.5.1   dplyr_1.1.4     purrr_1.0.4     readr_2.1.5    
[11] tidyr_1.3.1     tibble_3.2.1    ggplot2_3.5.2   tidyverse_2.0.0

loaded via a namespace (and not attached):
 [1] sass_0.4.10        utf8_1.2.5         generics_0.1.4     class_7.3-23      
 [5] KernSmooth_2.23-26 stringi_1.8.7      hms_1.1.3          digest_0.6.37     
 [9] magrittr_2.0.3     evaluate_1.0.3     grid_4.5.0         timechange_0.3.0  
[13] RColorBrewer_1.1-3 fastmap_1.2.0      rprojroot_2.0.4    jsonlite_2.0.0    
[17] e1071_1.7-16       DBI_1.2.3          scales_1.4.0       jquerylib_0.1.4   
[21] cli_3.6.5          rlang_1.1.6        crayon_1.5.3       units_0.8-7       
[25] bit64_4.6.0-1      withr_3.0.2        cachem_1.1.0       yaml_2.3.10       
[29] tools_4.5.0        parallel_4.5.0     tzdb_0.5.0         vctrs_0.6.5       
[33] R6_2.6.1           proxy_0.4-27       classInt_0.4-11    lifecycle_1.0.4   
[37] bit_4.6.0          vroom_1.6.5        pkgconfig_2.0.3    pillar_1.10.2     
[41] bslib_0.9.0        gtable_0.3.6       Rcpp_1.0.14        data.table_1.17.2 
[45] glue_1.8.0         xfun_0.52          tidyselect_1.2.1   rstudioapi_0.17.1 
[49] farver_2.1.2       htmltools_0.5.8.1  labeling_0.4.3     rmarkdown_2.29    
[53] compiler_4.5.0